/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package htsjdk.variant.variantcontext;
import htsjdk.variant.VariantBaseTest;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
/**
*
* @author aaron
*
* Class VariantJEXLContextUnitTest
*
* Test out parts of the VariantJEXLContext
*/
public class VariantJEXLContextUnitTest extends VariantBaseTest {
private static String expression = "QUAL > 500.0";
private static VariantContextUtils.JexlVCMatchExp exp;
Allele A, Aref, T, Tref;
Allele ATC, ATCref;
// A [ref] / T at 10
// - / ATC [ref] from 20-23
@BeforeClass
public void beforeClass() {
try {
exp = new VariantContextUtils.JexlVCMatchExp("name", VariantContextUtils.engine.get().createExpression(expression));
} catch (Exception e) {
Assert.fail("Unable to create expression" + e.getMessage());
}
}
@BeforeMethod
public void before() {
A = Allele.create("A");
Aref = Allele.create("A", true);
T = Allele.create("T");
Tref = Allele.create("T", true);
ATC = Allele.create("ATC");
ATCref = Allele.create("ATC", true);
}
@Test
public void testGetValue() {
Map<VariantContextUtils.JexlVCMatchExp, Boolean> map = getVarContext();
// make sure the context has a value
Assert.assertTrue(!map.isEmpty());
Assert.assertEquals(map.size(), 1);
// eval our known expression
Assert.assertTrue(!map.get(exp));
}
@Test(expectedExceptions=UnsupportedOperationException.class)
public void testContainsValue() {
Map<VariantContextUtils.JexlVCMatchExp, Boolean> map = getVarContext();
map.containsValue(exp);
}
@Test(expectedExceptions=UnsupportedOperationException.class)
public void testRemove() {
Map<VariantContextUtils.JexlVCMatchExp, Boolean> map = getVarContext();
map.remove(exp);
}
@Test(expectedExceptions=UnsupportedOperationException.class)
public void testEntrySet() {
Map<VariantContextUtils.JexlVCMatchExp, Boolean> map = getVarContext();
map.entrySet();
}
@Test(expectedExceptions=UnsupportedOperationException.class)
public void testClear() {
Map<VariantContextUtils.JexlVCMatchExp, Boolean> map = getVarContext();
map.clear();
}
/**
* helper method
* @return a VariantJEXLContext
*/
private JEXLMap getVarContext() {
List<Allele> alleles = Arrays.asList(Aref, T);
VariantContext vc = new VariantContextBuilder("test", "chr1", 10, 10, alleles).make();
return new JEXLMap(Arrays.asList(exp),vc);
}
}